Composable Visualization of High‐Dimensional Biological Data with ggalign
Wanyi Liu, Jia Ding, Yujun Sun, Bin Yan, Zhangyu Wang, Chunyang Wang, Chenyang Shu, Jian‐Guo Zhou, Guangchuang Yu, Yun Peng, Shixiang WangAbstract
ggalign is an R/CRAN package for creating flexible and composable multi‐panel data visualizations. The package extends the ggplot2 grammar of graphics by introducing an integrative framework that supports both data‐free and data‐aware composition. After five years of continuous development, ggalign has evolved into a comprehensive solution that handles diverse data types and layout structures, including quad, circular, and stack layouts. It was originally designed for general‐purpose composable visualization and has been expanded to support multi‐omics data integration, extending the application of ggalign to pan‐cancer analysis, single‐cell transcriptomics, and microbiome studies. This article presents eight basic protocols for constructing complex visualizations using the declarative syntax of ggalign. Basic Protocol 1 describes data‐free composition for flexible arrangement of multiple plots; Basic Protocol 2 describes data‐aware quad layout for integrating a central plot with surrounding annotations; Basic Protocol 3 describes data‐aware circular layout for visualizing ring‐structured data; Basic Protocol 4 describes stack layout and nested composition for coordinated display of multi‐track graphics; Basic Protocol 5 describes visualization of gene expression matrix heatmaps; Basic Protocol 6 describes visualization of somatic mutation landscapes using ggoncoplot(); Basic Protocol 7 describes circular visualization based on chromosome data, and Basic Protocol 8 describes cross‐connection visualization between genes and pathways. The complete package reference is available at
Basic Protocol 1 : Data‐free composition
Basic Protocol 2 : Aligning data‐aware with quad layouts
Basic Protocol 3 : Aligning data‐aware with circular layouts
Basic Protocol 4 : Stack layouts and nested composition
Basic Protocol 5 : Visualizing heatmap of gene expression matrix
Basic Protocol 6 : Visualizing somatic mutation landscapes using ggoncoplot()
Basic Protocol 7 : Visualizing circos plots with ggalign
Basic Protocol 8 : Visualizing observational connections